Creating a new pipeline

The create subcommand makes a new pipeline using the nf-core base template. With a given pipeline name, description and author, it makes a starter pipeline which follows nf-core best practices.

After creating the files, the command initialises the folder as a git repository and makes an initial commit. This first “vanilla” commit which is identical to the output from the templating tool is important, as it allows us to keep your pipeline in sync with the base template in the future. A full description of the file structure and all files created in the initial pipeline setup can be found here. See the nf-core syncing docs for more information on how the syncing works.

Once you have run the command, create a new empty repository on GitHub under your username (not the nf-core organisation, yet) and push the commits from your computer using the example commands in the above log. You can then continue to edit, commit and push normally as you build your pipeline.

Please see the nf-core documentation for a full walkthrough of how to create a new nf-core workflow.

[!TIP] As the log output says, remember to come and discuss your idea for a pipeline as early as possible! See the documentation for instructions.

Note that if the required arguments for nf-core create are not given, it will interactively prompt for them. If you prefer, you can supply them as command line arguments. See nf-core create --help for more information.

Customization

The nf-core create command comes with a number of options that allow you to customize the creation of a pipeline if you intend to not publish it as an nf-core pipeline. This can be done in two ways: by using interactive prompts, or by supplying a template.yml file using the --template-yaml <file> option. Both options allow you to specify a custom pipeline prefix to use instead of the common nf-core, as well as selecting parts of the template to be excluded during pipeline creation. The interactive prompts will guide you through the pipeline creation process. An example of a template.yml file is shown below.

name: coolpipe
description: A cool pipeline
author: me
prefix: myorg
skip:
  - github
  - ci
  - github_badges
  - igenomes
  - nf_core_configs

This will create a pipeline called coolpipe in the directory myorg-coolpipe (<prefix>-<name>) with me as the author. It will exclude all possible parts of the template:

• github: removed all files required for GitHub hosting of the pipeline. Specifically, the .github folder and .gitignore file.
• ci: removes the GitHub continuous integration tests from the pipeline. Specifically, the .github/workflows/ folder.
• github_badges: removes GitHub badges from the README.md file.
• igenomes: removes pipeline options related to iGenomes. Including the conf/igenomes.config file and all references to it.
• nf_core_configs: excludes nf_core/configs repository options, which make multiple config profiles for various institutional clusters available.

To run the pipeline creation silently (i.e. without any prompts) with the nf-core template, you can use the --plain option.